6-43777840-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003376.6(VEGFA):c.855+175C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 694,248 control chromosomes in the GnomAD database, including 36,382 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.32 (7816 hom., cov: 31)
  • Exomes 𝑓: 0.32 (28566 hom.)
• Consequence: VEGFA NM_003376.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.107

Genes affected

VEGFA (HGNC:12680): (vascular endothelial growth factor A) This gene is a member of the PDGF/VEGF growth factor family. It encodes a heparin-binding protein, which exists as a disulfide-linked homodimer. This growth factor induces proliferation and migration of vascular endothelial cells, and is essential for both physiological and pathological angiogenesis. Disruption of this gene in mice resulted in abnormal embryonic blood vessel formation. This gene is upregulated in many known tumors and its expression is correlated with tumor stage and progression. Elevated levels of this protein are found in patients with POEMS syndrome, also known as Crow-Fukase syndrome. Allelic variants of this gene have been associated with microvascular complications of diabetes 1 (MVCD1) and atherosclerosis. Alternatively spliced transcript variants encoding different isoforms have been described. There is also evidence for alternative translation initiation from upstream non-AUG (CUG) codons resulting in additional isoforms. A recent study showed that a C-terminally extended isoform is produced by use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism, and that this isoform is antiangiogenic. Expression of some isoforms derived from the AUG start codon is regulated by a small upstream open reading frame, which is located within an internal ribosome entry site. The levels of VEGF are increased during infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), thus promoting inflammation by facilitating recruitment of inflammatory cells, and by increasing the level of angiopoietin II (Ang II), one of two products of the SARS-CoV-2 binding target, angiotensin-converting enzyme 2 (ACE2). In turn, Ang II facilitates the elevation of VEGF, thus forming a vicious cycle in the release of inflammatory cytokines. [provided by RefSeq, Jun 2020]

POLR1C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 6-43777840-C-T is Benign according to our data. Variant chr6-43777840-C-T is described in ClinVar as [Benign]. Clinvar id is 1285895.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VEGFA	NM_003376.6	c.855+175C>T		intron_variant		ENST00000672860.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VEGFA	ENST00000672860.3	c.855+175C>T		intron_variant			NM_003376.6

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48524 AN: 151792 Hom.: 7811 Cov.: 31

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.347

GnomAD4 exome AF: 0.319 AC: 172932 AN: 542338 Hom.: 28566 Cov.: 7 AF XY: 0.317 AC XY: 89471 AN XY: 282230

Gnomad4 AFR exome AF: 0.335

Gnomad4 AMR exome AF: 0.345

Gnomad4 ASJ exome AF: 0.425

Gnomad4 EAS exome AF: 0.440

Gnomad4 SAS exome AF: 0.274

Gnomad4 FIN exome AF: 0.235

Gnomad4 NFE exome AF: 0.314

Gnomad4 OTH exome AF: 0.323

GnomAD4 genome AF: 0.320 AC: 48543 AN: 151910 Hom.: 7816 Cov.: 31 AF XY: 0.315 AC XY: 23397 AN XY: 74232

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.349

Alfa AF: 0.306 Hom.: 1075

Bravo AF: 0.336

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	9.3
Dann	Benign	0.65
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3024998; hg19: chr6-43745577; COSMIC: COSV57879506; COSMIC: COSV57879506;